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I just removed mine without replacing them. Am not sure what the drawbacks are though.
 
Basically, the supercap keeps the nvram powered when you replace the cr2032 coincell battery.
So with a supercap, you can replace that battery and all settings will stay.
Without it, your settings will be lost when you replace the battery.

If you only replace the battery when your settings get lost (because it's end of life), it doesn't really make a difference I assume.
 
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So I could just snip it off and it doesn't really matter?

What exactly does the nvram do?
 
Keep the system settings and game hiscores. system settings might also be in eeprom somewhere (as they don't change often)
eeprom has a limited number of write cycles. ram dosn't has that limit. If you keep it powered (with the cr2032 battery) it won't loose it's contents.
 
I have a naomi 1 and a 2 and I inspected around the supercap and everything looked ok, but I definitely don’t want to deal with what could happen if I leave them so I removed them from both.
 
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